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Insights into the evolution of dermal armour: osteoderms in a mammal, the spiny mouse

ABSTRACT: Insights into the evolution of dermal armour: osteoderms in a mammal, the spiny mouse

PROVIDER: PRJNA929296 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23268661_1.fastq.gz	Fastqsanger.gz
	SRR23268661_2.fastq.gz	Fastqsanger.gz
	SRR23268662_1.fastq.gz	Fastqsanger.gz
	SRR23268662_2.fastq.gz	Fastqsanger.gz
	SRR23268663_1.fastq.gz	Fastqsanger.gz

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Insights into the evolution of dermal armour: osteoderms in a mammal, the spiny mouse

Project description:The goals of this study are to compare NGS-derived transcriptomes (RNA-Seq) derived from skin sampled from the distal and the proximal regions. Using Acomys cahirinus we describe the structure and development of osteoderms in the tail which develop in a proximal to distal and dorsal to ventral sequence over a 6-week period postnatally. We use RNA sequencing to identify which gene regulatory networks are involved in their development which together suggests a deep molecular homology exists in the mammalian dermis which can be activated at any time in evolution.

2023-01-30 | GSE224007 | GEO

RNA-seq of of dermal fibroblasts

Project description:Dermal fibroblasts from human, rhesus macaque, mouse and rat, stimulated with dsRNA (poly I:C), interferon and controls. The innate immune response - the expression programme that is initiated once a pathogen is sensed - is known to be variable among responding cells, as well as to rapidly evolve in the course of mammal evolution. To study the transcriptional divergence and cell-to-cell variability of this response, we stimulated dermal fibroblast cells from two primates (human and macaque) and two rodents (mouse and rat) with dsRNA - a mimic of viral RNA that elicits a rapid innate immune response. Subsequently, we profiled the response using bulk RNA-seq, scRNA-seq and ChIP-seq across the four species and across different time points.

2018-07-06 | E-MTAB-5919 | biostudies-arrayexpress

Osteoderms in a mammal the spiny mouse Acomys and the independent evolution of dermal armor.

Project description:Osteoderms are bony plates found in the skin of vertebrates, mostly commonly in reptiles where they have evolved independently multiple times, suggesting the presence of a gene regulatory network that is readily activated and inactivated. They are absent in birds and mammals except for the armadillo. However, we have discovered that in one subfamily of rodents, the Deomyinae, there are osteoderms in the skin of their tails. Osteoderm development begins in the proximal tail skin and is complete 6 weeks after birth. RNA sequencing has identified the gene networks involved in their differentiation. There is a widespread down-regulation of keratin genes and an up-regulation of osteoblast genes and a finely balanced expression of signaling pathways as the osteoderms differentiate. Future comparisons with reptilian osteoderms may allow us to understand how these structures have evolved and why they are so rare in mammals.

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ChIP-seq of H3K4me3 and H3K27ac of dermal fibroblasts

Project description:Dermal fibroblasts from human, rhesus macaque, mouse and rat with and without dsRNA (poly I:C) stimulation (1ug/mL for 4 hours). The innate immune response - the expression programme that is initiated once a pathogen is sensed - is known to be variable among responding cells, as well as to rapidly evolve in the course of mammal evolution. To study the transcriptional divergence and cell-to-cell variability of this response, we stimulated dermal fibroblast cells from two primates (human and macaque) and two rodents (mouse and rat) with dsRNA - a mimic of viral RNA that elicits a rapid innate immune response. Subsequently, we profiled the response using bulk RNA-seq, scRNA-seq and ChIP-seq across the four species and across different time points.

2018-07-06 | E-MTAB-5918 | biostudies-arrayexpress

single-cell RNA-seq of of dermal fibroblasts

Project description:Dermal fibroblasts from human, rhesus macaque, mouse and rat, stimulated with dsRNA (poly I:C) in a time course of 0,2,4 and 8 hours, profiled using the Smart-seq2 protocol. The innate immune response - the expression programme that is initiated once a pathogen is sensed - is known to be variable among responding cells, as well as to rapidly evolve in the course of mammal evolution. To study the transcriptional divergence and cell-to-cell variability of this response, we stimulated dermal fibroblast cells from two primates (human and macaque) and two rodents (mouse and rat) with dsRNA - a mimic of viral RNA that elicits a rapid innate immune response. Subsequently, we profiled the response using bulk RNA-seq, scRNA-seq and ChIP-seq across the four species and across different time points.

2018-07-06 | E-MTAB-5920 | biostudies-arrayexpress

Single-cell RNA-seq of of dermal fibroblasts (second replicate)

Project description:Dermal fibroblasts from human, rhesus macaque, mouse and rat, stimulated with dsRNA (poly I:C) in a time course of 0,4 and 8 hours, profiled using the Smart-seq2 protocol. The innate immune response - the expression programme that is initiated once a pathogen is sensed - is known to be variable among responding cells, as well as to rapidly evolve in the course of mammal evolution. To study the transcriptional divergence and cell-to-cell variability of this response, we stimulated dermal fibroblast cells from two primates (human and macaque) and two rodents (mouse and rat) with dsRNA - a mimic of viral RNA that elicits a rapid innate immune response. Subsequently, we profiled the response using bulk RNA-seq, scRNA-seq and ChIP-seq across the four species and across different time points.

2018-07-06 | E-MTAB-6066 | biostudies-arrayexpress

Single-cell RNA-seq of of dermal fibroblasts using microfluidic droplet capture (unstimulated cells)

Project description:The innate immune response - the expression programme that is initiated once a pathogen is sensed - is known to be variable among responding cells, as well as to rapidly evolve in the course of mammal evolution. To study the transcriptional divergence and cell-to-cell variability of this response, we stimulated dermal fibroblast cells from two primates (human and macaque) and two rodents (mouse and rat) with dsRNA - a mimic of viral RNA that elicits a rapid innate immune response. Subsequently, we profiled the response using bulk RNA-seq, scRNA-seq and ChIP-seq across the four species and across different time points. This experiment contains data of dermal fibroblasts from 3 human individuals, unstimulated, sequenced by 10X Genomics technology. Corresponding data from stimulated cells are found under ArrayExpress accession <a href="/arrayexpress/experiments/E-MTAB-5989">E-MTAB-5989</a>.

2018-07-06 | E-MTAB-5988 | biostudies-arrayexpress

Single-cell RNA-seq of of dermal fibroblasts using microfluidic droplet capture (stimulated cells)

Project description:The innate immune response - the expression programme that is initiated once a pathogen is sensed - is known to be variable among responding cells, as well as to rapidly evolve in the course of mammal evolution. To study the transcriptional divergence and cell-to-cell variability of this response, we stimulated dermal fibroblast cells from two primates (human and macaque) and two rodents (mouse and rat) with dsRNA - a mimic of viral RNA that elicits a rapid innate immune response. Subsequently, we profiled the response using bulk RNA-seq, scRNA-seq and ChIP-seq across the four species and across different time points. This experiment contains data of dermal fibroblasts from 3 human individuals, stimulated with dsRNA (poly I:C) for 6 hours, sequenced by 10X Genomics technology. Corresponding data from unstimulated cells are found under ArrayExpress accession <a href="/arrayexpress/experiments/E-MTAB-5988">E-MTAB-5988</a>.

2018-07-06 | E-MTAB-5989 | biostudies-arrayexpress

mammal metagenome

Project description:mammal metagenome Genome sequencing and assembly

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Comparative Transcriptomic Analysis of Dermal Wound Healing Reveals De Novo Skeletal Muscle Regeneration in Acomys cahirinus

Project description:This project is a comprehensive analysis of gene expression following full-thickness excisional dermal wounds in the African spiny mouse and the laboratory mouse.

2019-04-25 | GSE113081 | GEO

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